Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004317.1 Corchorus olitorius cultivar O-4 contig04330, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 737

Length: 1229
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37


Found at i:351 original size:88 final size:88

Alignment explanation


    Indices: 243--427  Score: 345
    Period size: 88  Copynumber: 2.1  Consensus size: 88

        233 GAATTCTCAT

                *                                                            
        243 TTAGATATTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGAGTTTGTTTGTTGGG
          1 TTAGCTATTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGAGTTTGTTTGTTGGG

                                   
        308 GAAGCGGTTTGTTGGCTCATAGA
         66 GAAGCGGTTTGTTGGCTCATAGA

                                                                             
        331 TTAGCTATTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGAGTTTGTTTGTTGGG
          1 TTAGCTATTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGAGTTTGTTTGTTGGG

                *                  
        396 GAAGGGGTTTGTTGGCTCATAGA
         66 GAAGCGGTTTGTTGGCTCATAGA

                      
        419 TTAGC-ATTT
          1 TTAGCTATTT

        428 CGGAATTGTA


Statistics
Matches: 95,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  87    4  0.04
  88   91  0.96

ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43


Consensus pattern (88 bp):   
TTAGCTATTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGAGTTTGTTTGTTGGG
GAAGCGGTTTGTTGGCTCATAGA

Found at i:507 original size:3 final size:3

Alignment explanation


    Indices: 501--535  Score: 54
    Period size: 3  Copynumber: 12.0  Consensus size: 3

        491 TTTAATAATA

                                         *                 
        501 TAT TAT TAT TAT TAT TAT TAT TTT TAT TA- TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

        536 AAAGAGGGAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2    2  0.07
   3   27  0.93

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TAT

Done.